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Fix MQ calculation #262

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merged 2 commits into from
Sep 23, 2020
Merged

Fix MQ calculation #262

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10f367a
Fix MQ calculation
jkgoodrich Sep 23, 2020
ad3800f
Add to CHANGELOG.md
jkgoodrich Sep 23, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
* Fixed handling of missing entries (not within a ref block / alt site) when computing `coverage_stats` in `sparse_mt.py` [[#242]] (/~https://github.com/broadinstitute/gnomad_methods/pull/242)
* Fix for error in `compute_stratified_sample_qc` where `gt_expr` caused error [(#259)](/~https://github.com/broadinstitute/gnomad_methods/pull/259)
* Add reference genome to call of `has_liftover` in `get_liftover_genome` [(#259)](/~https://github.com/broadinstitute/gnomad_methods/pull/259)
* Added fix for MQ calculation in `_get_info_agg_expr`, switched `RAW_MQ` and `MQ_DP` in calculation [(#262)](/~https://github.com/broadinstitute/gnomad_methods/pull/262)

## Version 0.4.0 - July 9th, 2020

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4 changes: 2 additions & 2 deletions gnomad/utils/sparse_mt.py
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Expand Up @@ -238,10 +238,10 @@ def _agg_list_to_dict(
mq_tuple = agg_expr.pop(f"{prefix}RAW_MQandDP")
elif f"{prefix}RAW_MQ" in agg_expr and f"{prefix}MQ_DP" in agg_expr:
logger.info(
f"Computing {prefix}MQ as sqrt({prefix}MQ_DP/{prefix}RAW_MQ). "
f"Computing {prefix}MQ as sqrt({prefix}RAW_MQ/{prefix}MQ_DP). "
f"Note that MQ will be set to 0 if {prefix}RAW_MQ == 0."
)
mq_tuple = (agg_expr.pop(f"{prefix}MQ_DP"), agg_expr.pop(f"{prefix}RAW_MQ"))
mq_tuple = (agg_expr.pop(f"{prefix}RAW_MQ"), agg_expr.pop(f"{prefix}MQ_DP"))

if mq_tuple is not None:
agg_expr[f"{prefix}MQ"] = hl.cond(
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